When computing the iface for parts of the protein complex, which interact with each other, the complex surface should only contain the chains of interest.
For example, Complex_id1 has 5 chains.
We are looking at the interaction between id1_AB and id1_CD parts, however the surface for the Complex_id1 still contains a fifth chain (E). This way we will wrongly label some parts of the id1_AB and id1_BC surfaces as interfaces because they are being covered by an extra chain.
I am assuming we only want to look at interfaces between the parts we know that interact, so I am assuming that using the full complex surface is not the right way to label the interfaces.
When computing the iface for parts of the protein complex, which interact with each other, the complex surface should only contain the chains of interest.
For example, Complex_id1 has 5 chains.
We are looking at the interaction between id1_AB and id1_CD parts, however the surface for the Complex_id1 still contains a fifth chain (E). This way we will wrongly label some parts of the id1_AB and id1_BC surfaces as interfaces because they are being covered by an extra chain.
I am assuming we only want to look at interfaces between the parts we know that interact, so I am assuming that using the full complex surface is not the right way to label the interfaces.